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Perpendicularity of circles on a curved surface

I am measuring a part that has a curved surface which also happens to be the D datum. I scanned this surface to measure the surface profile of it. This curved surface also has two holes on it which have a perpendicularity call out using the D datum. I have no idea how to go about measuring this. It won't let me output the perpendicularity measurement on the report. I get a message that says "For perpendicularity tolerances, the nominal considered features must be perpendicular to the primary nominal datum." Is this because the surface is curved and therefore impossible to be perpendicular to these holes?